|
| Status |
Public on Jul 20, 2015 |
| Title |
3'-Seq C2C12-D |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 cells_Differentiated
|
| Organism |
Mus musculus |
| Characteristics |
cell type: myoblast
cell line: C2C12
culture status: differentiation (D)
|
| Treatment protocol |
Differentiated cells were transferred to DMEM containing 2% horse serum upon reaching confluence and harvested 48 h later.
|
| Growth protocol |
Cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 20% fetal bovine serum. Undifferentiated cells were harvested at 60–70% confluence.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample preparations for 3′-seq was performed as previously reported (Lianoglou et al., Genes & Development, 2013) using total RNA extracted from 8 week-old C57BL/6 male mouse tissue, including testis, liver, brain, and skeletal muscle.
3'-seq libraries were prepared for sequencing using previously reported protocol(Lianoglou et al., Genes & Development, 2013).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Protocol: 3'-seq
|
| Data processing |
Illumina RTA 1.17 software used for basecalling.
Sequenced reads were mapped to the mouse genome (mm9) with STAR alignment software (Dobin et al., 2013) and the parameter “--outFilterMultimapNmax 1 --alignIntronMax 1” (no multi-hit reads, no splice prediction) to treat poly-A containing reads.
Quantification of each gene was performed by counting the number of reads that were mapped around the 3′-UTR region and then normalizing the number as reads per million (RPM) per region. In the case of novel histone H3 variant genes, the region within 3 kb from the end of a coding sequence was defined as the putative 3'-UTR.
genome build: mm9
processed data files format and content: tab-delimited text files include RPKM values for each Sample
processed data file: 3primeSeq_RPMTable_rep2.txt.gz
|
| |
|
| Submission date |
Dec 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yasuyuki Ohkawa |
| E-mail(s) |
yohkawa@bioreg.kyushu-u.ac.jp
|
| Organization name |
Kyushu University
|
| Department |
Medical Institute of Bioregulation, Medical Institute of Bioregulation
|
| Street address |
3-1-1 Maidashi, Higashi-ku, Fukuoka
|
| City |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE63890 |
Characterization of mouse histone H3 variants |
|
| Relations |
| BioSample |
SAMD00019360 |
| SRA |
DRX020527 |
